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2012-03-23 11:30:27 +0200	commented answer	Manually compiled R segfaults @kcrisman: it tells me that I need at least 50 points of reputation to do that.
2012-03-23 09:51:59 +0200	answered a question	Manually compiled R segfaults So, it seems it is a compiler bug. Compiling on gcc 4.6 went fine with my default flags.
2012-03-15 11:17:20 +0200	commented question	Manually compiled R segfaults @kcrisman: i started bisecting the flags yesterday only to find that there's another compilation error (compiler reports bug in its own code) that shows on gcc 4.4 (which is installed on that VPS), but not on 4.5. I might find some time during the weekend to check it, but it's not a big priority to me now... I'll probably try getting gcc 4.7 on that VPS and recompile everything just to be sure. For now I use R compiled with `-O0` and it is good enough for my purposes.
2012-03-14 16:52:29 +0200	marked best answer	Sage from precompiled package -- R plots You would need to reinstall the R spkg. `sage -f r` should do the trick.
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2012-03-14 11:04:02 +0200	commented question	Manually compiled R segfaults @kcrisman: updated. However even when launching R by itself I get a crash, and it shouldn't require much memory for itself.
2012-03-13 17:24:57 +0200	received badge	● Editor (source)
2012-03-13 17:24:05 +0200	asked a question	Manually compiled R segfaults Hello, My R crashes when I try to compile it manually. This is the output of `make` when trying to compile `sagemath` from scratch: gcc -std=gnu99 -I../../../../include -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/home/liori/sage/sage-4.8/l e -L/home/liori/sage/sage-4.8/local/lib/ -march=nocona -O2 -fomit-frame-pointer -s -pipe -c md5.c -o md5.o gcc -std=gnu99 -I../../../../include -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/home/liori/sage/sage-4.8/l e -L/home/liori/sage/sage-4.8/local/lib/ -march=nocona -O2 -fomit-frame-pointer -s -pipe -c signals.c -o signals.o gcc -std=gnu99 -shared -L/home/liori/sage/sage-4.8/local/lib/ -o tools.so text.o init.o Rmd5.o md5.o signals.o -L../../../../li make[8]: Entering directory `/home/liori/sage/sage-4.8/spkg/build/r-2.14.0.p1/src/src/library/tools/src' make[8]: `Makedeps' is up to date. make[8]: Leaving directory `/home/liori/sage/sage-4.8/spkg/build/r-2.14.0.p1/src/src/library/tools/src' make[8]: Entering directory `/home/liori/sage/sage-4.8/spkg/build/r-2.14.0.p1/src/src/library/tools/src' mkdir -p -- ../../../../library/tools/libs make[8]: Leaving directory `/home/liori/sage/sage-4.8/spkg/build/r-2.14.0.p1/src/src/library/tools/src' make[7]: Leaving directory `/home/liori/sage/sage-4.8/spkg/build/r-2.14.0.p1/src/src/library/tools/src' make[6]: Leaving directory `/home/liori/sage/sage-4.8/spkg/build/r-2.14.0.p1/src/src/library/tools' * caught segfault * address 0x7fff17a1f090, cause 'memory not mapped' aborting ... /bin/bash: line 1: 9951 Done echo "tools:::.install_package_description('.', '"../../../library/tools"')" 9952 Segmentation fault \| R_DEFAULT_PACKAGES=NULL ../../../bin/R --vanilla --slave > /dev/null Same thing when I tried to use a binary `sagemath` distribution and just recompile R there using `./sage -f r`. When R is run as standalone binary, it crashes right after printing invitation text. I launched it with `.../R --debugger gdb` and printed backtrace: [...] Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. Program received signal SIGSEGV, Segmentation fault. strchrnul () at ../sysdeps/x86_64/strchrnul.S:34 34 ../sysdeps/x86_64/strchrnul.S: No such file or directory. in ../sysdeps/x86_64/strchrnul.S Current language: auto The current source language is "auto; currently asm". (gdb) bt #0 strchrnul () at ../sysdeps/x86_64/strchrnul.S:34 #1 0x00007ffff712cd2f in __find_specmb (s=0x7fffffff9a00, format=0x7ffffffff028 <Address 0x7ffffffff028 out of bounds>, ap=0x7fffffffbb80) at printf-parse.h:99 #2 _IO_vfprintf_internal (s=0x7fffffff9a00, format=0x7ffffffff028 <Address 0x7ffffffff028 out of bounds>, ap=0x7fffffffbb80) at vfprintf.c:1325 #3 0x00007ffff71524f2 in _IO_vsnprintf (string=0x7fffffff9b80 "", maxlen=<value optimized out>, format=0x7ffffffff028 <Address 0x7ffffffff028 out of bounds>, args=0x7fffffffbb80) at vsnprintf.c:120 #4 0x00007ffff793671b in Rvsnprintf () from /home/liori/sage/sage-4.8/spkg/build/r-2.14.0.p1/src/lib/libR.so #5 0x00007ffff7939d5f in Rf_warning () from /home/liori/sage/sage-4.8/spkg/build/r-2 ... (more)
2012-03-13 11:26:14 +0200	asked a question	Sage from precompiled package -- R plots Hello, I installed Sage on my Debian Squeeze server using `sage-4.8-linux-64bit-ubuntu_10.04.3_lts-x86_64-Linux.tar.lzma` package. I wanted to use it mostly for R, and therefore tried some plotting, but I get the known `X11 is not available` message. I installed packages recommended here in other questions, such as `xorg-dev`, `libpango1.0-dev` and `libcairo2-dev`, and restarted the worksheet, but with no results. Do I need to recompile `sage` now?